3.2 Sex chromosomes and autosomes
Male and female Illumina paired-end reads were mapped separately to genomic scaffolds to estimate MRPM. The MRPM value of female reads for chrX1, chrX2 and chrX3 were 1,439,092, 1,333,387 and 1,051,602, whereas those for the corresponding male reads were 781,901, 726,210 and 576,946 respectively. As expected, MRPM values of female reads were roughly twice as high as those of male reads in chrX1, chrX2 and chrX3. For the other 10 chromosomes, no significant difference in total reads was observed between females and males, with the female-to-male ratio ranging from 0.90 to 1.00 (Table S5).
It has been shown that the X chromosome is conserved in aphids while chromosomal rearrangements are common for autosomes (Li et al. 2021, Mathers et al. 2021). The syntenic blocks were compared between theS. chinensis assembly and that of Ac. pisum from Macrosiphini (Li, et al., 2020), R. maidis from Aphidini (Chen et al. 2019), and E. lanigerum from Eriosomatinae (Figure 3B). The comparisons revealed high levels of genome rearrangements between autosomes. The three S. chinensis chromosomes were mapped to the conserved X chromosome of Macrosiphini and Aphidini, and two X chromosomes of E. lanigerum . The observed multiple X chromosomes were consistent with previous reports (Biello et al., 2020), which were speculated to result from the fragmentation of the X chromosome inS. chinensis and E. lanigerum or from the ancient fusion event of the large X chromosome in Aphidinae (Macrosiphini + Aphidini). This observation strongly supports that chrX1, chrX2 and chrX3 are the sex chromosomes and the karyotype of S. chinensis is XX+X (Yuan et al., 2021).